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121,910 results • Page 48 of 2439
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Identification of SSR markers from RNA-seq data
MISA SSR-markers data RNA-seq
9 months ago by Kutti • 0
4
votes
9
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1.9k
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Super enhancer calling using ROSE for mm39 genome: list index out of range error
ChIP-Seq super-enhancers ROSE mm39
9 months ago by Gayatri • 0
0
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1
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571
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assembling human mitochondrial genomes with nanopore long reads
ONT assembly genome mitochondria nanopore
9 months ago by eebloom ▴ 110
5
votes
12
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7.9k
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how can i download human ribosomal reference ?
RNA-Seq rRNA
updated 9 months ago by ▴ 430 • written 6.3 years ago by ▴ 70
2
votes
4
replies
877
views
How should the order of microbiome data preprocessing be prioritized?
aggregation microbiome preprocess normalization filter
9 months ago by ssko ▴ 20
6
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10
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2.3k
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6 follow
High Detection of Duplication in RNAseq dataset
Deduplication RNAseq
updated 9 months ago by 22k • written 12 months ago by • 0
0
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6
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1.7k
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What should I do if death cell counts and types biologically important in my single cell data?
scRNA cell-death single-cell
updated 9 months ago by 22k • written 12 months ago by ▴ 50
0
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1
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1.0k
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Salmon low mapping rates
Reference Mapping Salmon RNA-seq
updated 9 months ago by • 0 • written 15 months ago by • 0
0
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3
replies
1.3k
views
Removing gDNA contamination from RNA seq data
contamination gDNA
updated 9 months ago by 22k • written 12 months ago by • 0
0
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2
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865
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dorado and modkit for m6A identification
dorado m6A modkit
9 months ago by baibhu1234 ▴ 60
0
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0
replies
320
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cnvkit results with start positions always 0 ?
cnvkit variant-calling
updated 9 months ago by 45k • written 9 months ago by • 0
0
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0
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511
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Regression and scaling in scanpy
scanpy
9 months ago by bioinfo ▴ 160
0
votes
2
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644
views
Question about metabolic pathway prediction using only DNA sequencing data
metabolism genomics ngs
updated 9 months ago by ▴ 60 • written 9 months ago by ▴ 60
1
vote
6
replies
1.2k
views
English terms distinguishing genotype allelic nucleotides (T/C) from VCF encoded genotype (0/1)
genotypes vcf
9 months ago by Jeremy Leipzig 23k
0
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0
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417
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How to define a clonotype by its TCR sequencing data with its own structure.
TCR sequencing clonotype scRNA
9 months ago by diqixiaoyaoer ▴ 20
4
votes
2
replies
897
views
Getting fasta sequence for a gene
fasta regulatory genome region gene
updated 9 months ago by 103k • written 9 months ago by ★ 4.4k
1
vote
3
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923
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Identification of variants from Spatial Transcriptomics using STARSolo
spatial-transcriptomics STAR visium
updated 9 months ago by 45k • written 9 months ago by ▴ 160
0
votes
6
replies
1.5k
views
Seurat Mito Prefix Removed from Features
Seurat
updated 9 months ago by ▴ 820 • written 9 months ago by • 0
0
votes
1
reply
682
views
Is there a way to write a genbank file in R?
R Genbank Genetics BioConductor
updated 9 months ago by ▴ 820 • written 9 months ago by • 0
11
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7
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1.7k
views
6 follow
Forum: How people usually perform scRNA Seq Analysis on HPC?
hpc Single-cell cluster scRNA-Seq
updated 9 months ago by 45k • written 9 months ago by ▴ 10
1
vote
2
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1.3k
views
Is it possible to get the percentage identity between a pair of orthologs at the proteome level with the Orthology Matrix (OMA)?
OMA Sequence-identity
updated 9 months ago by 45k • written 9 months ago by • 0
8
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9
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1.4k
views
Can we construct single pangenome for different crops
pangenome different crops
updated 9 months ago by ▴ 490 • written 9 months ago by ▴ 70
0
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0
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308
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For RNAseq GSA analysis with unique rodent species
GOenrichment RNAseq GSA hypergeometrictest Apodemus
9 months ago by ohtang7 ▴ 40
6
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4
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1.0k
views
heterozygous variant on the X chromosome
xchrom variant vcf heterozygous
9 months ago by ashaneev07 ▴ 50
3
votes
4
replies
1.6k
views
m6A modification prediction using Nanopore DRS data (RNA004)
m6A DRS Nanopore
7 months ago by baibhu1234 ▴ 60
5
votes
9
replies
1.4k
views
Database like Cellxgene for well-annotated atlas
mapping reference
updated 9 months ago by 89k • written 9 months ago by • 0
1
vote
1
reply
464
views
Insert sequence in plasmid (plasmidid)
plasmidid insert WGS
updated 9 months ago by 166k • written 9 months ago by • 0
2
votes
2
replies
782
views
How to remove pseudo genes from a list
Expression gene differential names
9 months ago by Meghan.T ▴ 10
2
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7
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1.3k
views
DESeq2 normalizing against two baselines
normalization deseq2 rnaseq
updated 9 months ago by 105k • written 9 months ago by • 0
4
votes
0
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21k
views
Herald: The Biostar Herald for Monday, December 09, 2024
herald
9 months ago by Biostar 3.6k
0
votes
4
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914
views
Split Visium spatial fastq according to barcodes
spatial visium barcodes fastq
9 months ago by ThaiosX195 • 0
1
vote
3
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731
views
Public databases and raw counts
Normalisation counts databases
updated 9 months ago by 103k • written 9 months ago by • 0
1
vote
1
reply
578
views
Python methylation position visualisation
python plotting visualisation help methylation
updated 9 months ago by ★ 3.1k • written 9 months ago by • 0
3
votes
3
replies
910
views
Can I trust this script I wrote for assembling plant genomes?
assembly genome. script plant genomics
updated 9 months ago by 56k • written 9 months ago by ▴ 10
0
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1
reply
555
views
Help using enricher function from clusterProfiler
R clusterProfiler ORA enrichment
updated 9 months ago by ▴ 820 • written 9 months ago by • 0
3
votes
1
reply
970
views
pvalueCutoff for enrichGO, enrichKEGG and enrichDO does not seem to function properly
clusterprofiler
9 months ago by t.mcgovern • 0
0
votes
0
replies
416
views
STAR pair-end gene count discrepancy vs. RSEM
star genecount rsem htseq illumina
9 months ago by cropero • 0
3
votes
5
replies
1.3k
views
How to remove duplicated SNPs based on MAF with Plink?
SNPs Plink2 duplication maf
updated 8 months ago by 11k • written 9 months ago by ▴ 30
1
vote
2
replies
682
views
linear pangenome for crops
pangenome linear
updated 9 months ago by ▴ 20 • written 9 months ago by ▴ 70
0
votes
2
replies
960
views
model interaction in DeSeq2 with >1K samples
DeSeq2 interaction large sample set design
updated 9 months ago by 22k • written 9 months ago by • 0
0
votes
2
replies
645
views
Single Copy lncRNA
lncRNA Single Copy
9 months ago by Kutti • 0
1
vote
6
replies
1.3k
views
Concatenating all unmapped or alternative contigs in a reference genome
contigs fasta reference
updated 9 months ago by ▴ 60 • written 9 months ago by ▴ 20
1
vote
8
replies
1.5k
views
Feature Counts - potential bug with outfile.jcounts
FeatureCounts
9 months ago by chrisk • 0
0
votes
1
reply
827
views
log transformation before imputation (impute.knn) in proteomic data?
proteomic log_transformation impute.knn
updated 9 months ago by ▴ 130 • written 9 months ago by ★ 1.3k
0
votes
2
replies
871
views
Spatial correlation between two continuous variables
spatial transcriptomics correlation
updated 9 months ago by ★ 7.7k • written 9 months ago by • 0
5
votes
6
replies
1.2k
views
IGV is not showing all alignments of SAM file
IGV
9 months ago by gernophil ▴ 130
1
vote
6
replies
1.2k
views
Multimapping Reads to be counted or not
lowcounts featureCounts RNASeq Multimapping
updated 9 months ago by 153k • written 9 months ago by ▴ 70
0
votes
1
reply
704
views
How to create modified basecalling dataset with nanopore data with an ambiguous motif sequence?
dorado nanopore remora
updated 9 months ago by 153k • written 9 months ago by • 0
1
vote
2
replies
722
views
How to visualize shared pathways between ORA (enrichment) results?
visualization ora pathways enrichment
9 months ago by Picasa ▴ 690
7
votes
2
replies
813
views
How Can Pathway Analysis Methods Account for Genes with Different Activation Roles?
gsea functional-analysis pathway-enrichment
updated 9 months ago by 153k • written 9 months ago by ▴ 30
121,910 results • Page 48 of 2439
Recent Votes
GSEA vs GO enrichment
Blastn and Kraken2 short reads clssification
Live Online course: Bioinformatic tools for transcriptomic data, Oct 2025
Tried building a compact sequence format with 4-bit storage
Comment: Tried building a compact sequence format with 4-bit storage
Answer: Tried building a compact sequence format with 4-bit storage
Tried building a compact sequence format with 4-bit storage
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Answer: Trouble when installing arb by SilentGene ▴ 120
I've got the same error when installing from `arb-6.0.6-source.tgz` and `arb-7.0-source.tgz`. Anyone has any solution?
Comment: Hifiasm is getting killed while trying to assemble a genome by pranavdatar01 • 0
Yes, I did check for adaptor contamination, and did not find any. I have kept all the reads with quality score of more than 30.
Comment: Hifiasm is getting killed while trying to assemble a genome by Panos ★ 1.8k
No overlapping reads? Have you checked for contamination?
Comment: Tried building a compact sequence format with 4-bit storage by Pranava ▴ 10
I see, but the reason I was planning on using a 4bit system is so that there wouldn't be too much data loss but thank you for the suggesti…
Comment: Splice junctions plots for long-read seq data by alison.ludzki • 0
Thank you! I will check out miso!
Comment: Hifiasm is getting killed while trying to assemble a genome by pranavdatar01 • 0
I did subsample the data to 30x coverage. I did run hifiasm on it, the log file did show some contents, but hifiasm ended again, stating th…
Comment: Tried building a compact sequence format with 4-bit storage by Alex Reynolds 36k
Using four bits for storage won't beat 2bit, of course, but direct access to a sequence of interest sounds interesting and useful and might…
Comment: Hifiasm is getting killed while trying to assemble a genome by Panos ★ 1.8k
Why don't you subsample your HiFi reads and try running hifiasm again? Maybe this will help if you have memory problems. However, I haven't…
Comment: Is total miRNA in EV constant? Implications for library size normalization. by Gordon Smyth ★ 8.3k
RNA-seq is very good at relative analyes. It would be straightforward to determine which miRNAs are relatively more abundant, compared to o…
Comment: Tried building a compact sequence format with 4-bit storage by Pranava ▴ 10
Woah!!! Thank you very much, Matthias. I honestly didn't even know some of those existed and I will definitely go through them and try to u…
Answer: Tried building a compact sequence format with 4-bit storage by Matthias Zepper 5.1k
Hello Pranava, Thanks for sharing your repository. Devising a new file format is an interesting undertaking and certainly a task with many…
Answer: Gene Ontology Enrichment with LOC gene IDs in Common Carp (Cyprinus carpio) by GenoMax 153k
`LOC` gene ID's are often assigned to uncharacterized genes and you may not get useful information from databases for them, thus they will …
Comment: Whole Genome Sequencing IG regions by GenoMax 153k
> are the calls I am seeing reliable or should I take them with something of a pinch of salt? Not sure what calls you are referring to but…
Comment: RNA-SEQ where only a subset of genes is of interest by piffelpaff • 0
Sorry to revive this ancient thread but I'm currently discussing the same question with some people in my lab and would love to somebody po…
Answer: STARlong for pacbio Isoseq reads by YuZJ • 0
Hello, you may try deSALT (DOI: 10.1186/s13059-019-1895-9, GitHub: ydLiu-HIT/deSALT) or uLTRA (DOI: 10.1093/bioinformatics/btab540, GitHub:…
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